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Structure of the RNA pyrophosphohydrolase BdRppH in complex with dGTP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 7 298 PEG 4000, Na acetate, pH 7, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.08 60.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.446 α = 90 b = 68.448 β = 90 c = 92.74 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD adsc Q210 2008-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.0 NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.4 46.37 89.2 0.049 32.267 6.6 15730
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 40.7 0.691 4.4 695
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2.6 46.37 13703 686 98.32 0.243 0.24 0.2265 0.297 0.281 RANDOM 58.584
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 2.15 2.57 -4.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.206 r_dihedral_angle_4_deg 18.665 r_dihedral_angle_3_deg 18.398 r_dihedral_angle_1_deg 6.326 r_scangle_it 1.796 r_angle_refined_deg 1.246 r_scbond_it 1.092 r_mcangle_it 0.747 r_mcbond_it 0.439 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.206 r_dihedral_angle_4_deg 18.665 r_dihedral_angle_3_deg 18.398 r_dihedral_angle_1_deg 6.326 r_scangle_it 1.796 r_angle_refined_deg 1.246 r_scbond_it 1.092 r_mcangle_it 0.747 r_mcbond_it 0.439 r_nbtor_refined 0.309 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.159 r_symmetry_vdw_refined 0.133 r_symmetry_hbond_refined 0.122 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2131 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 62
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection AMoRE phasing